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Dr Emma Hodcroft Profile picture
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12 Mar, 4 tweets, 2 min read
🗓️CoVariants.org is now updated to data from 11 Mar!🗓️

Plus, 2 new variants, and new additions to the Shared Mutations page!

⚙️The builds are already updated and live!🔍

1/4
First, the S:Q677 USA variants S:677H (Robin1) and S:677P (Pelican) are added to the lists of variants & Per Country plots.

These variants arose at the end of 2020 & are found across the US, but prominently in the north-central & south-central USA (respectively).

2/4
We know the Shared Mutations table has been helpful for many people to compare Spike mutations shared between Variants - & now it's got even more variants! 🎉

Sort by commonness or position & see what keeps popping up.
We aim to add even more soon!

3/4
covariants.org/shared-mutatio…
Finally, a tiny but happy celebration for 20E (EU1), which now has a proper badge just like its siblings 🥳

As always, thanks to @ivan_aksamentov who endlessly ensures that all I envisage for CoVariants becomes a reality!

4/4

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Dr Emma Hodcroft Profile picture
10 Mar
🗓️CoVariants.org now updated to data from 9 Mar🗓️

Plus, 2 new variants and 5 new mutations added!

Let's have a look at what's new...

1/10
To help track variants of interest, we've added 20C/S:484K (B.1.526, sometimes called the 'New York variant') & 20A/S:484K (B.1.525)!

2/10
20C/S:484K (blue) carries the S:E484K mutation as well as a mutation at S:A701V (shared with 501Y.V2). Interestingly, 2 independent sister-clades nearby (yellow) do *not* have 484, but have S:S477N (same mutation as is in 20A.EU2 & 20F.

3/10

covariants.org/variants/20C.S…
Read 10 tweets
Dr Emma Hodcroft Profile picture
4 Mar
All the focal builds linked from CoVariants.org are now updated with data from 2 Mar.

This includes the new focal builds for 501Y.V1, 501Y.V2 & 501Y.V3 (B.1.1.7, B.1.351, P.1) - links in the thread....

1/7
501Y.V1 (B.1.1.7) is still significantly downsampled due to the extremely high number of sequences in this cluster - but the focal build helps a bit!

2/7
nextstrain.org/groups/neherla…
501Y.V2 is not downsampled much now, which means it gives a pretty good view of where the variant has spread. Shown in large dots here are the clusters in Mayotte, the French territory off the coast of Africa (yellow circle near Africa).

3/7
nextstrain.org/groups/neherla…
Read 7 tweets
Dr Emma Hodcroft Profile picture
3 Mar
📅CoVariants.org is updated with data from 2 March📅, as well as a very exciting new change:

Variants & mutations are now separated & clearly labelled - & each Variant of Concern has it's own page & data! 🎉

1/8
A new, improved left-menu now clearly indicates whether a page is concerned with a Variant (collection of mutations in one part of the tree) or a Mutation (one change, could be in many places on the tree).

Updated naming helps, too!
And menus collapse to keep things tidy.

2/8
And to help you find what you're looking for - a table to help you link up nomenclature!! 🎉

A lot of people have asked for this - it's not yet beautiful but it's already hopefully useful.

And you can go straight to the CoV-Lineages reports on the 3 main VoCs, too!

3/8
Read 8 tweets
Dr Emma Hodcroft Profile picture
24 Feb
While not downplaying our current careful situation, I think we've got a lot to be optimistic about in 2021, if we can think globally 🌍 & act appropriately 💉😷

I thoroughly enjoyed reading this interview with @fabiennekatrin: '1 year of #SARSCoV2'

1/5
blick.ch/schweiz/epidem…
On conspiracy theories:
"Unfortunately, conspiracy theories have become very dominant in the pandemic. I can understand: [they often] provide much simpler explanations. We scientists should learn from this, to make what we say more accessible and understandable."

2/5
On mutations:
"If many people have already been infected, it is an advantage for a virus [to evade] this immunity. A year ago that would not have been of any use to the virus. But now... we just have to be aware that the pandemic is not static. It is constantly changing."

3/5
Read 5 tweets
Dr Emma Hodcroft Profile picture
19 Feb
📅CoVariants.org is now updated with data up to the 18th Feb! 📅

Plus! A new mutation has been added 😉

And we've had another few neat feature tweaks thanks to some great contributors!

1/6
Enough recent data has come through to push the graphs to the next 2-week mark (they're plotted by sequences per 2-week period to help avoid weekly jitters), so the most recent data point is the 8th Feb now (covering the period two weeks after this).

2/6
Linking with our recent preprint on the S:Q677 variants, S:Q677 is now included on CoVariants!

We can particularly see 677 showing up clearly in the USA 'Per Country' graphs.

3/6
Read 7 tweets
Dr Emma Hodcroft Profile picture
16 Feb
Tweets haven't been happening as times get busy, but CoVariants.org is now updated to data from 15 Feb! Focal builds are in the oven 🥖

This update also includes some neat new improvements - let's take a quick look!

1/4
Thanks to @jamesscottbrown, pages are now a little tidier, with the link icons placed after the links!

Thanks to a suggestion by @theosanderson the proportion of 'other' variants on the 'Per Country' page are now grey - easier to see and label!

2/4 ImageImage
@ivan_aksamentov has helped greatly improve the 'Per Variants' page! Tool-tip legends now show the lines so you can see the difference between solid & dashed!

And you can now select what kind or order you'd like the legend to show - frequency or country!

3/4 ImageImage
Read 4 tweets

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